[Bioperl-l] bioperl-db and postgres

Hilmar Lapp hlapp@gnf.org
Sun, 24 Nov 2002 13:39:55 -0800

The HOWTO is somewhat dated, I haven't touched that yet. Basically, 
sequences live in a namespace, and it is up to you for your local 
database how much sense you want the namespace to make. You can put 
everything under namespace bioperl if you don't care at all, or you 
may want to choose namespaces that more or less reflect where those 
guys came from.

The constraints are that accession and version have to be unique 
within a namespace. These days not many dbs use accessions that 
would clash with accessions of others (in fact, I'm not aware of 
any), so you may be fine with just dumping everything under the same 

I'll integrate the patch Yves sent today. You will need an anonymous 
cvs checkout, or a cvs update (don't forget -d) if you have an 
existing checkout.  Post if you need help with that.


On Friday, November 22, 2002, at 03:40 AM, Anthony Underwood wrote:

> Hi all,
> I am trying to set up a postgres database and enter sequences using the
> load_seqdatabase.pl. Being fairly new to databases I am a bit confused
> by the options. I understand that I need to create a database named
> biosql with the postgres schema. However I also have read in the HOWTO:
> (in the bioperl-db docs) that it is important to specify a dataset
> identifier. In this way it says that many 'biodatabases' can be stored
> in a single biosql instance.
> Having looked at the load_seqdatabase.pl script I am not sure how this
> can be specified and am confused by what the difference is between
> database (which is set to biosql and can not be changed by command line
> options) and dbname  (which is set by default to biosql but can be
> changed in the options).
> Please can anybody clarify this terminology (specifically dataset
> identifier, database and dbname). The namespace option is a bit
> mystifying to me also. Should that be left as bioperl?
> On an aside, what is the best way to apply the postgres patch that was
> posted a few days ago on this mailing list? Should I download the
> bioperl-db tarball and put that in the appropriate place in the perl
> directory and then some how apply the patch?
> Sorry to be so clueless on these items but I am a biologist with only
> self-taught knowledge of perl etc.
> Many thanks in advance,
> Anthony Underwood
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757